DNA-(Apurinic or Apyrimidinic Site) Lyase: A DNA repair enzyme that catalyses the excision of ribose residues at apurinic and apyrimidinic DNA sites that can result from the action of DNA GLYCOSYLASES. The enzyme catalyzes a beta-elimination reaction in which the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. This enzyme was previously listed under EC 3.1.25.2.Apurinic Acid: Hydrolysate of DNA in which purine bases have been removed.Deoxyribonuclease IV (Phage T4-Induced): An enzyme which catalyzes the endonucleolytic cleavage of phosphodiester bonds at purinic or apyrimidinic sites (AP-sites) to produce 5'-Phosphooligonucleotide end products. The enzyme prefers single-stranded DNA (ssDNA) and was formerly classified as EC 3.1.4.30.Carbon-Oxygen Lyases: Enzymes that catalyze the cleavage of a carbon-oxygen bond by means other than hydrolysis or oxidation. EC 4.2.PolynucleotidesN-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Endodeoxyribonucleases: A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.DNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.Deoxyribonuclease (Pyrimidine Dimer): An enzyme which catalyzes an endonucleolytic cleavage near PYRIMIDINE DIMERS to produce a 5'-phosphate product. The enzyme acts on the damaged DNA strand, from the 5' side of the damaged site.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.DNA-Formamidopyrimidine Glycosylase: A DNA repair enzyme that is an N-glycosyl hydrolase with specificity for DNA-containing ring-opened N(7)-methylguanine residues.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Purines: A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.ATP Citrate (pro-S)-Lyase: An enzyme that, in the presence of ATP and COENZYME A, catalyzes the cleavage of citrate to yield acetyl CoA, oxaloacetate, ADP, and ORTHOPHOSPHATE. This reaction represents an important step in fatty acid biosynthesis. This enzyme was formerly listed as EC 4.1.3.8.Lyases: A class of enzymes that catalyze the cleavage of C-C, C-O, and C-N, and other bonds by other means than by hydrolysis or oxidation. (Enzyme Nomenclature, 1992) EC 4.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Kinetics: The rate dynamics in chemical or physical systems.Methyl Methanesulfonate: An alkylating agent in cancer therapy that may also act as a mutagen by interfering with and causing damage to DNA.DNA Polymerase beta: A DNA repair enzyme that catalyzes DNA synthesis during base excision DNA repair. EC 2.7.7.7.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Deoxycytidine Monophosphate: Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Polysaccharide-Lyases: A group of carbon-oxygen lyases. These enzymes catalyze the breakage of a carbon-oxygen bond in polysaccharides leading to an unsaturated product and the elimination of an alcohol. EC 4.2.2.Adenylosuccinate Lyase: An enzyme that, in the course of purine ribonucleotide biosynthesis, catalyzes the conversion of 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole to 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole and the conversion of adenylosuccinic acid to AMP. EC 4.3.2.2.Ribosemonophosphates: Ribose substituted in the 1-, 3-, or 5-position by a phosphoric acid moiety.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Exodeoxyribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Exonucleases: Enzymes that catalyze the release of mononucleotides by the hydrolysis of the terminal bond of deoxyribonucleotide or ribonucleotide chains.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Oxo-Acid-Lyases: Enzymes that catalyze the cleavage of a carbon-carbon bond of a 3-hydroxy acid. (Dorland, 28th ed) EC 4.1.3.DeoxyriboseUracilHypertrophy: General increase in bulk of a part or organ due to CELL ENLARGEMENT and accumulation of FLUIDS AND SECRETIONS, not due to tumor formation, nor to an increase in the number of cells (HYPERPLASIA).Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.DNA Ligases: Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD).DioxolanesNucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.DNA Polymerase I: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.Pyrimidine Dimers: Dimers found in DNA chains damaged by ULTRAVIOLET RAYS. They consist of two adjacent PYRIMIDINE NUCLEOTIDES, usually THYMINE nucleotides, in which the pyrimidine residues are covalently joined by a cyclobutane ring. These dimers block DNA REPLICATION.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.GuanineAldehyde-Lyases: Enzymes that catalyze a reverse aldol condensation. A molecule containing a hydroxyl group and a carbonyl group is cleaved at a C-C bond to produce two smaller molecules (ALDEHYDES or KETONES). EC 4.1.2.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.Borohydrides: A class of inorganic or organic compounds that contain the borohydride (BH4-) anion.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.DNA Adducts: The products of chemical reactions that result in the addition of extraneous chemical groups to DNA.Osmium Tetroxide: (T-4)-Osmium oxide (OsO4). A highly toxic and volatile oxide of osmium used in industry as an oxidizing agent. It is also used as a histological fixative and stain and as a synovectomy agent in arthritic joints. Its vapor can cause eye, skin, and lung damage.Glycolates: Derivatives of ACETIC ACID which contain an hydroxy group attached to the methyl carbon.Phosphorus-Oxygen Lyases: Enzymes that catalyze the cleavage of a phosphorus-oxygen bond by means other than hydrolysis or oxidation. EC 4.6.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Flap Endonucleases: Endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Hydroxylamines: Organic compounds that contain the (-NH2OH) radical.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).Cell Extracts: Preparations of cell constituents or subcellular materials, isolates, or substances.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Deoxyguanosine: A nucleoside consisting of the base guanine and the sugar deoxyribose.Lucanthone: One of the SCHISTOSOMICIDES, it has been replaced largely by HYCANTHONE and more recently PRAZIQUANTEL. (From Martindale The Extrapharmacopoeia, 30th ed., p46)Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Mutagens: Chemical agents that increase the rate of genetic mutation by interfering with the function of nucleic acids. A clastogen is a specific mutagen that causes breaks in chromosomes.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
  • We have used a genetic approach in Saccharomyces cerevisiae to determine whether or not AP sites are blocks to DNA replication and the biological consequences if AP sites persist in the genome. (duke.edu)
  • Experiments with different substrates demonstrated that the protein covalently binds to the 5′ DNA product, i.e. the fragment containing an α,β-unsaturated aldehyde. (biochemj.org)
  • Much of the seminal work elucidating these repair systems has taken advantage of defined DSB substrates, either constructed in vitro or formed in cells by site-specific nucleases [ 9 ]. (hindawi.com)
  • Associations between lung cancer risk and common polymorphisms in the DNA repair genes xeroderma pigmentosum complementation group D (XPD), X-ray repair cross-complementing group 1 (XRCC1), XRCC3 and apurinic/apyrimidinic endonuclease/redox factor 1 were examined within a randomized clinical trial designed to determine whether alpha-tocopherol, beta-carotene, or both would reduce cancer incidence among male smokers in Finland. (nih.gov)
  • Our results suggest that common alterations in single DNA repair genes are not major determinants of lung cancer susceptibility among smokers. (nih.gov)
  • We report here the biochemical characterization of ROS1 and the effect of its overexpression on the DNA methylation of target genes. (pnas.org)
  • DNA cytosine methylation is important for many epigenetic processes including X chromosome inactivation, genomic imprinting, epigenetic changes during carcinogenesis, and silencing of transposons, of specific genes during development and of certain transgenes ( 1 - 5 ). (pnas.org)
  • Therefore, we genotyped nine single-nucleotide polymorphisms (SNPs) in six genes encoding BER proteins. (medscimonit.com)
  • Genetic variation in the DNA repair genes might be associated with altered DNA repair capacities (DRC). (nih.gov)
  • There is growing evidence describing DNA repair genes polymorphisms are related to increased cancer risk including colorectal cancer (CRC). (cdc.gov)
  • Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. (nih.gov)
  • Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes. (nih.gov)
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.5 Classification:TRANSCRIPTION Release Date:2018-02-28 Deposition Date:2018-02-05 Revision Date: Molecular Weight:55137.11 Macromolecule Type:Protein Residue Count:474 Atom Site Count:3899 DOI:10.2210/pdb6cc0/pdb Abstract: Pseudomonas aeruginosa is an opportunistic pathogen that uses the process of quorum sensing (QS) to coordinate the expression of many virulence genes. (mendeley.com)
  • Researchers have also identified that mutations that have lead to changes in PNKP, similar to mutations in other genes that encode other strand break repair proteins, have been connected to a severe autosomal recessive neurological disorder. (wikibooks.org)
  • YB-1 is a DNA- and RNA-binding protein that regulates expression of many important genes. (semanticscholar.org)
  • Shows robust 3-5 exonuclease activity on 3-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. (genecards.org)
  • The altered DNA base, and in some cases a few nucleotides adjacent to the altered base, is removed by excision, and the DNA is repaired by DNA synthesis and ligation. (els.net)
  • The deletion of nth1 in the apn2 mutant strain partially relieves the MMS sensitivity of the apn2 single mutant, indicating that the Apn2 and Nth1 act in the same pathway for the repair of abasic sites. (biomedsearch.com)
  • Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. (ox.ac.uk)
  • We have analyzed the effect of solute carrier family 2 (facilitated glucose transporter), member 1 polymorphisms on 2-[fluorine-fluoro-2-deoxy-D-glucose-uptake with a combination of polymorphisms of hypoxia-inducible factor 1 alpha, apurinic/apyimidinic endonuclease, and vascular endothelial growth factor A in a hypoxia-related pathway. (cdc.gov)
  • Repair of nuclear and mitochondrial oxidative DNA lesions occurs predominantly through the base excision repair (BER) pathway ( 37 ). (asm.org)
  • To improve the treatment of women with ovarian cancer, we are investigating the modulation of a prominent DNA-damaging agent, temozolomide, by manipulating the DNA base excision repair (BER) pathway via BER inhibitor, methoxyamine, and overexpression of N -methylpurine DNA glycosylase (MPG). (aacrjournals.org)
  • We are focusing on inhibition and manipulation of the DNA base excision repair (BER) pathway in ovarian cancer. (aacrjournals.org)
  • Methoxyamine is an alkoxyamine derivative able to block the single nucleotide BER pathway by reacting with the aldehyde group in the acyclic sugar left in the DNA abasic site following the glycosylase-driven removal of a damaged nucleotide ( 6 , 7 ). (aacrjournals.org)
  • These radiation resistant thermophiles are resistant to desiccation as well and maintain their homeostasis by advance DNA repair mechanisms, reactive oxygen species (ROS) detoxification system and accumulation of compatible solutes. (bireme.br)
  • The genome exerts its functions through interactions with proteins. (elsevier.com)
  • Hence, comprehensive identification of protein-occupied sites by genomic footprinting is critical to an in-depth understanding of genome functions. (elsevier.com)
  • DMS added to the culture medium readily enters the cell and methylates its DNA throughout the genome except for the regions bound by proteins, thereby obviating the need for nuclear isolation in genomic footprinting. (elsevier.com)
  • Umeyama, T & Ito, T 2018, ' DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers ', Current Protocols in Molecular Biology , vol. 123, no. 1, e60. (elsevier.com)
  • Mitochondria are eukaryotic organelles that share bacterial features such as a double-membrane structure and a circular multi-copied genome or mitochondrial DNA (mtDNA). (frontiersin.org)
  • With the development of high-throughput sequencing technologies, such as two-hybrid systems and mass spectrometry technology for pairwise protein interactions, large-scale PPI networks of E. coli can be constructed at genome level [ 20 ]. (biomedcentral.com)
  • On the basis of the three‐dimensional structure and taking account of previous biochemical experiments, we propose a DNA‐binding mode and reaction mechanism for MutM. (embopress.org)
  • The mutM ( fpg ) gene encoding the MutM protein is highly conserved across a wide range of aerobic bacteria. (embopress.org)
  • In addition to generating the bulk of the cell's energy supply mitochondria are important sites of calcium homeostasis, nucleotide and amino acid metabolism and biosynthesis of heme, iron-sulfur clusters, and ubiquinone. (frontiersin.org)
  • A protein complex is formed by the interaction of more than two functional related peptide chains through disulfide bonds or other proteins, so it performs some given biological functions. (biomedcentral.com)
  • Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. (rcsb.org)
  • The interaction is important for DNA repair, as auto-ribosylation is necessary to assemble and activate multiprotein complexes to carry out the process [ 6 , 7 ]. (mdpi.com)
  • However, in heterodimeric complexes with its partner basic helix-loop-helix proteins, BETA2 does not appear to be a strong activator of transcription by itself. (asm.org)
  • CD81), heat shock proteins, components of the endosomal sorting complexes required for transport (ESCRT), integrins and regulators of intracellular trafficking (e.g. (biomedcentral.com)
  • The identification of protein complexes and functional modules of E. coli is essential to reveal the principles of cell organization, process, and function. (biomedcentral.com)
  • At present, many studies focus on the detection of E. coli protein complexes based on experimental methods. (biomedcentral.com)
  • However, based on the large-scale proteomics data set of E. coli, the simultaneous prediction of protein complexes and functional modules, especially the comparative analysis of them is relatively less. (biomedcentral.com)
  • In this study, the Edge Label Propagate Algorithm (ELPA) of the complex biological network was used to predict the protein complexes and functional modules of two high-quality PPI networks of E. coli , respectively. (biomedcentral.com)
  • Some novel and significant protein complexes and functional modules were revealed based on ELPA. (biomedcentral.com)
  • Moreover, through a comparative analysis of predicted complexes with corresponding functional modules, we found the protein complexes were significantly overlapped with corresponding functional modules, and almost all predicted protein complexes were completely covered by one or more functional modules. (biomedcentral.com)
  • Finally, on the same PPI network of E. coli , ELPA was compared with a well-known protein module detection method (MCL) and we found that the performance of ELPA and MCL is comparable in predicting protein complexes. (biomedcentral.com)
  • In this paper, a link clustering method was used to predict protein complexes and functional modules in PPI networks of E. coli , and the correlation between them was compared, which could help us to understand the molecular functional units of E. coli better. (biomedcentral.com)
  • Experiments and data analysis (algorithmic model) are two effective methods to identify protein complexes and functional modules of E. coli . (biomedcentral.com)
  • Revealing protein complexes and functional modules in the E. coli PPI network is an important research topic to understand the essential biological functions of proteins. (biomedcentral.com)
  • However, with the release of some high-throughput E. coli PPI datasets in recent years, it has become possible to predict protein complexes and functional modules of E. coli based on complex network models. (biomedcentral.com)
  • AP lyase works by cleaving the phosphodiester bond 5' to the abasic site by a β-elimination reaction to give a β-unsaturated aldehyde attached to 3'-phosphate at one terminus and a 5'-phosphate at the other. (wikibooks.org)
  • Does also incise at AP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of R-loop structures, and single-stranded RNA molecules. (rcsb.org)
  • DNA strand displacement and excessive gap filling during DNA repair were observed in cell-free extracts of an XRCC1-deficient mutant cell line, in agreement with the results from the reconstituted system. (nih.gov)
  • Removes the blocking groups from the 3'-termini of the DNA strand breaks generated by ionizing radiations and bleomycin. (genesilico.pl)
  • Most DNA double-strand breaks (DSBs) formed in a natural environment have chemical modifications at or near the ends that preclude direct religation and require removal or other processing so that rejoining can proceed. (hindawi.com)
  • DNA strand breaks are often caused by internal and external factors. (wikibooks.org)
  • Incompletely repaired methoxyamine-blocked AP sites lead to increases in single-strand breaks and double-strand breaks (DSB) as well as cell death ( 4 , 11 ). (aacrjournals.org)
  • The fragment MS Protein Standard represents a new category of using heavy isotope labeled (15N, 13C) Lysine and Arginine residues resulting in more than 99% isotope incorporation, as internal MS standards offering distinct advantages to existing products for relative and absolute quantification. (creative-proteomics.com)
  • These findings confirm the classification of ALKBH1 as an AP lyase, identify the primary and a secondary lysine residues involved in the lyase reaction, and demonstrate that the protein forms a covalent adduct with the 5′ DNA product. (biochemj.org)
  • abstract = "The genotoxic, extracellular accumulation of amyloid β (Aβ) protein and subsequent neuronal cell death are associated with Alzheimer's disease (AD). (utmb.edu)